overlap = params.overlap
datadir = params.download_path
imgs_l = []
dest_base = params.download_path
with Cytomine(host=host, public_key=public_key,
private_key=private_key) as cytomine:
res = {}
annotations = AnnotationCollection()
annotations.project = id_project
annotations.showWKT = True
annotations.showMeta = True
annotations.showGIS = True
annotations.showTerm = True
annotations.showImage = True
annotations.fetch()
print(annotations)
for annotation in annotations:
print("ID: {} | Img: {} | Pjct: {} | Term: {} ".format(
annotation.id, annotation.image, annotation.project,
annotation.term))
if len(annotation.term) == 1:
if (annotation.term[0], annotation.image) not in res.keys():
res[(annotation.term[0], annotation.image)] = []
res[(annotation.term[0],
annotation.image)].append(loads(annotation.location))
last = res[(annotation.term[0], annotation.image)][-1]
print(last.bounds, last.to_wkt().count(","))
ks = res.keys()
def get_images_mask_per_annotation_per_user(proj_id, image_id, user_id,
scale_factor, dest):
im = ImageInstanceCollection()
im.project = proj_id
im.image = image_id
im.fetch_with_filter("project", proj_id)
image_width = int(im[0].width)
image_height = int(im[0].height)
print(image_height, image_width)
annotations = AnnotationCollection()
annotations.project = proj_id
annotations.image = image_id
annotations.user = user_id
annotations.showWKT = True
annotations.showMeta = True
annotations.showTerm = True
annotations.showGIS = True
annotations.showImage = True
annotations.showUser = True
annotations.fetch()
dct_anotations = {}
for a in annotations:
print(a.user)
if len(a.term) == 1:
term = a.term[0]
if term not in dct_anotations:
dct_anotations[term] = []
dct_anotations[term].append(a.location)
else:
warnings.warn("Not suited for multiple or no annotation term")
for t, lanno in dct_anotations.items():
result_image = Image.new(mode='1',
size=(int(image_width * scale_factor),
int(image_height * scale_factor)),
color=0)
for pwkt in lanno:
if pwkt.startswith("POLYGON"):
label = "POLYGON"
elif pwkt.startswith("MULTIPOLYGON"):
label = "MULTIPOLYGON"
coordinatesStringList = pwkt.replace(label, '')
if label == "POLYGON":
coordinates_string_lists = [coordinatesStringList]
elif label == "MULTIPOLYGON":
coordinates_string_lists = coordinatesStringList.split(
')), ((')
coordinates_string_lists = [
coordinatesStringList.replace('(', '').replace(')', '')
for coordinatesStringList in coordinates_string_lists
]
for coordinatesStringList in coordinates_string_lists:
# create lists of x and y coordinates
x_coords = []
y_coords = []
for point in coordinatesStringList.split(','):
point = point.strip(
string.whitespace) # remove leading and ending spaces
point = point.strip(
string.punctuation
) # Have seen some strings have a ')' at the end so remove it
x_coords.append(round(float(point.split(' ')[0])))
y_coords.append(round(float(point.split(' ')[1])))
x_coords_correct_lod = [
int(x * scale_factor) for x in x_coords
]
y_coords_correct_lod = [
image_height * scale_factor - int(x * scale_factor)
for x in y_coords
]
coords = [
(i, j)
for i, j in zip(x_coords_correct_lod, y_coords_correct_lod)
]
# draw the polygone in an image and fill it
ImageDraw.Draw(result_image).polygon(coords, outline=1, fill=1)
result_image.save(params.dest + '/' + str(t) + '.png')